Wat causes the screen to pause and windows to temp freeze?

This problem has occurred over a few years and with a number of Gnome distributions, including Ubuntu and Fedora, and it just won't go away.

I just installed Ubuntu 10.10 / Gnome. Almost immediately, windows that opened would grey out and temporarily freeze. The mouse can still move, most of the time. The greying of windows can happen frequently or not a all for a while. The freezing can last a few seconds or many. This inconsistency makes it difficult for me to figure out what is triggering this problem.